Project description:We isolated and sequenced small RNA profiles in THP-1 cells, including total, nuclear, cytoplasmic, and exosomal repertoires, as well as monitored small RNA dynamics during THP-1 differentiation and in response to Pol III inhibitor ML-60218
Project description:We detect the small RNAs subcellular distribution in breast cancer cell lines MCF-7 and MDA-MB-231, and normal cell line MCF-10A. Each cell line, we detected the nuclear and cytoplasmic small RNAs expression intensity; and then we could get the nuclear-cytoplasmic-ratio.
Project description:We developed an extensive resource of RNAseq data to track mRNA maturation across subcellular locations in multiple cell types. Mouse embryonic stem cells, neuronal progenitor cells, and post-mitotic neurons were separated into chromatin-associated, soluble nucleoplasmic and cytoplasmic fractions, with RNA from each fraction isolated as both polyadenylated, total rRNA-depleted pools, and small RNA pools and sequenced. Genes exhibit disparate patterns of RNA enrichment between subcellular fractions, with some genes maintaining more polyadenylated RNA in the chromatin fraction than in the cytoplasm. These chromatin-associated poly(A)+ RNAs are often incompletely spliced and we devise a simple metric to identify introns whose excision is posttranscriptional. X-means clustering and deep learning methods identified intron groups with four defined regulatory behaviors, including complete cotranscriptional splicing, and complete retention in the cytoplasmic RNA. Two groups display intermediate levels of retention in the RNA in the nucleus but are fully spliced in the cytoplasm. These groups include previously described sets of retained introns, but extend to many new introns, including introns repressed by polypyrimidine track binding protein 1 (PTBP1). We find that the PTBP1 regulated Gabbr1 transcript is highly expressed in mESC without expression of Gabbr1 protein. The bulk of Gabbr1 RNA is incompletely spliced and remains sequestered on chromatin similar to certain long noncoding RNAs. Only after neuronal differentiation does Gabbr1 RNA become fully processed and released to the cytoplasm as mRNA. Thus, splicing repression and the chromatin anchoring of RNA provide a combined mechanism of posttranscriptional regulation over development. Our datasets provide a rich resource for analyzing many other aspects of mRNA maturation in subcellular locations and across development.
Project description:Background: Macrophages represent an important part of the immune system in the intestine and are crucial for maintaining homeostasis. As part of research investigating the effect of dietary fibres on the intestinal immune barrier THP-1 macrophages were used as model system. Methods: THP-1 monocytes were stimulated for 48 hours with 100 ng/ml PMA and 48 hours rested in medium. Subsequently, they were stimulated with 500 ug/ml dietary fibres and the maximal observed LPS contamination to serve as background control. After 6 hours, total RNA was extracted and Affymterix Human Gene 1.1 ST arrays were used to analyze the gene expression profiles. To identify dietary fibre induced gene expression profiles in dietary fibre gene responses were compared to medium samples. Furthermore, to analyse differentiatlly affected pathways Ingenuite Pathway Analysis was employed. Results: There was a clear difference in significantly differentially expressed genes (gene cut-off p<0.05) with beta-glucan oat medium viscosity and GOS changing transcription of a relative small amount of genes and Sugar beet pectin and Resistant starch a relative large amount of genes. These latter two were also the only dietary fibres to demonstrate an increase in Fc-receptor-related pathway activation. Alternatively, beta-glucan oat medium viscosity and GOS were the only dietary fibres to activate pathways related to cellular movement and the only two to not activate the Ahr-signaling pathway (p<0.05). Conclusion: our data indicate that the in vitro THP-1 macrophage model can be used to differentiate in immunomodulatory potential of dietary fibres and provide hypotheses for functional differentiation.
Project description:Expression profiling of LY6E-silent THP-1 cells (THP-1-shLY6E) and control cells (THP-1-shCtrl). Results provide evidence that LY6E is effectively knocked down in THP-1shLY6E, compared to THP-1-shCtrl, and show the different expressed genes following LY6E silence in THP-1 cells. Total RNA obtained from 2 cell lines.
Project description:THP-1 macrophages were treated with EVs and stimulated with LPS, and then total RNA was extracted from cells. Extracted total RNAs were investigated by microarray analysis. Increase and decrease of mRNA expression were investigated between EV-treated and non-treated THP-1 macrophages.
Project description:Acquisition of a new strain of non-typeable Haemophilus influenzae (NTHi) is often associated with exacerbation of chronic obstructive pulmonary disease (COPD). We have previously reported that COPD patients who are homozygous null for SIGLEC14 gene is less susceptible to COPD exacerbation than those who have wild-type allele with functional SIGLEC14 gene. In order to gain insight into the mechanism behind the COPD exacerbation, and to find new clues that may lead to the discovery of objective biomarker of COPD exacerbation, Siglec-14/THP-1 and Siglec-5/THP-1 cell lines, which mimic monocytes from homozygous wild-type and homozygous SIGLEC14-null person, respectively, were incubated with or without NTHi, and their gene expression profiles were compared by using Affymetrix Human Genome U133 Plus 2.0 Array.
Project description:Expression profiling of LY6E-silent THP-1 cells (THP-1-shLY6E) and control cells (THP-1-shCtrl). Results provide evidence that LY6E is effectively knocked down in THP-1shLY6E, compared to THP-1-shCtrl, and show the different expressed genes following LY6E silence in THP-1 cells.